def is_exec(program):
"""checks if a program is in the global path and executable"""
cmd = ['which', program]
try:
return procOps.call_proc_lines(cmd)[0].endswith(program)
except ProcException:
return False
def samtools_version():
"""checks the version of samtools installed"""
try:
r = procOps.call_proc_lines(['samtools', '--version'])
if StrictVersion(r[0].split()[1].split('-')[0]) < '1.3':
raise ToolMissingException('samtools version is not >= 1.3.0')
except ProcException:
raise ToolMissingException('samtools is not installed')
def samtools_version():
"""checks the version of samtools installed"""
try:
r = procOps.call_proc_lines(['samtools', '--version'])
if StrictVersion(r[0].split()[1].split('-')[0]) < '1.3':
raise ToolMissingException('samtools version is not >= 1.3.0')
except ProcException:
raise ToolMissingException('samtools is not installed')
def get_tree(hal):
"""
Extracts a Tree object from a HAL
:param hal: HAL file.
:return: Tree object
"""
cmd = ['halStats', '--tree', hal]
newick = call_proc_lines(cmd)[0]
return ete3.Tree(newick, format=1)
def get_tree(hal):
"""
Extracts a Tree object from a HAL
:param hal: HAL file.
:return: Tree object
"""
cmd = ['halStats', '--tree', hal]
newick = call_proc_lines(cmd)[0]
return ete3.Tree(newick, format=1)
def is_exec(program):
"""checks if a program is in the global path and executable"""
if running_in_container():
# We assume containerized versions don't need to check if the
# tools are installed--they definitely are, and calling docker
# just to run "which" can be surprisingly expensive. But we do
# check for the presence of Docker, since that should take
# only a few ms.
cmd = ['which', 'docker']
pl = Procline(cmd, stdin='/dev/null', stdout='/dev/null', stderr='/dev/null')
try:
pl.wait()
except ProcException:
raise ToolMissingException("Docker not found. Either install Docker, or install CAT's dependencies and use --binary-mode local.")
cmd = ['which', program]
try:
return procOps.call_proc_lines(cmd)[0].endswith(program)
except ProcException:
return False